Decontaminating genomic data for accurate species delineation and hybrid detection in the Lasius ant genus

Species identification and delineation by molecular methods has become a widely used technique and has revealed hybrids between species previously believed to be completely reproductively isolated. However, the application of molecular methods is associated with a risk of DNA contamination, which can result in the identification of false hybrids and generate inaccurate conclusions about the species' identities and characteristics. Here, we generate and analyze a dataset of nuclear SNP data and mitochondrial DNA sequences from over 1,000 Lasius ants to accurately investigate the species delineation and hybridization proclivity within the genus. We describe an approach, based on a combination of competitive mapping and allelic depth ratio analysis, that allows us to identify DNA contaminations and filter them from large-scale datasets. By applying this approach to the Lasius ants, we are able to remove interspecific contamination, and to clearly delineate each species genetically as well as identify a hybrid individual between L. emarginatus and L. platythorax.